Pre-designed Xenium Gene Expression Panels

The Xenium platform uses targeted panels to detect gene expression at subcellular resolution. The Xenium v1 pre-designed panels were designed to cover the major cell types for specific tissues. They consist of genes selected from single cell atlas data, research area experts, and literature searches.

Consult either the Xenium In Situ Gene Expression - Probe Hybridization, Ligation & Amplification User Guide (CG000582) or Xenium In Situ Gene Expression with Cell Segmentation Staining User Guide (CG000749) to execute the workflow.

Additional resources

Download and explore 10x Genomics public datasets that use pre-designed and add-on custom panels here. Xenium panel part numbers (PN) are provided here.

Click here to generate a custom panel with the Xenium Panel Designer. Find answers to frequently asked questions here.

Table of contents

Pre-designed panel information

The table below provides the following information for available pre-designed Xenium gene expression panels:

Panel name and the number of targeted genes
Downloadable panel metadata with gene name, transcript ID, number of probe sets, number of codewords for each target, and cell type annotation in CSV format (see below for details).
Downloadable gene_panel JSON file for each panel (format described here).
Panel probe sequences in FASTA format and the genomic coordinates of the panel probe sequences in 13-column detailed BED format (see glossary for details).

Panel	Genes targeted	Panel metadata and JSON	Probe genomic target sequences and coordinates
Xenium Human Brain Gene Expression Panel	266	CSV, JSON	FASTA, BED
Xenium Human Breast Gene Expression Panel	280	CSV, JSON	FASTA, BED
Xenium Human Colon Gene Expression Panel	322	CSV, JSON	FASTA, BED
Xenium Human Immuno-Oncology Profiling Panel	380	CSV, JSON	FASTA, BED
Xenium Human Lung Gene Expression Panel	289	CSV, JSON	FASTA, BED
Xenium Human Multi-Tissue and Cancer Panel	377	CSV^*, JSON	FASTA, BED
Xenium Human Skin Gene Expression Panel	260	CSV, JSON	FASTA, BED
Xenium Mouse Brain Gene Expression Panel	247	CSV, JSON	FASTA, BED
Xenium Mouse Tissue Atlassing Panel	379	CSV^*, JSON	FASTA, BED

*The Xenium Human Multi-Tissue and Cancer Panel and Xenium Mouse Tissue Atlassing Panel were developed to accommodate multiple human or mouse tissue types, respectively. Genes can be specifically expressed in different cell types, depending on the tissue context, and this is reflected in the annotation column of the CSV file. For example, the annotation "Breast - Breast glandular cells" indicates that this gene is expressed in that cell type, which is only present in breast tissue. Other cell types that are shared between multiple tissues were grouped under a "General" category. For example, the annotation "General - T cells" indicates that this gene is expressed in T cells, which are present in multiple tissues. You can use the annotations column to view the subset of genes targeted for specific tissue type(s) in your experiment, along with the "General" tissue category.

Panel negative controls

Each pre-designed panel contains 40 negative control codewords and 20 negative control targets (except the Xenium Mouse Brain Gene Expression Panel, which has 27).

For negative control targets, multiple probes are designed for each non-biological target sequence. It follows the same design process as for real target sequences, with a goal of reaching eight probe sets per target (for more detail, read the Getting Started with Xenium Panel Design page). An add-on custom panel will have the same number of negative control probe sets as the pre-designed panel it is based upon.

Decoding and negative controls are described on the Xenium Onboard Analysis algorithms page.

Custom panel information

Please read the Getting Started with Xenium Panel Design page for information about supported add-on custom and standalone custom gene panel options.

Panel metadata

For each of the pre-designed panels, a metadata file is provided on this page (CSV format). This file contains additional panel information, which may be helpful for designing your experiment or custom add-on genes.

Column	Description
Gene	The gene identifier targeted by the probe.
Ensembl ID	The Ensembl gene identifier targeted by the probe.
Number of Probe sets	The number of probe sets targeting each isoform of the gene.
Codewords	The number of codewords used to decode each gene.
Annotation	The 10x Genomics cell type annotation given to each gene based on single cell atlas data, research area experts, and literature searches.

Next Steps

Return to panel design landing page

Document Type: Xenium v1 Panel Information
Last Modified: March 13, 2024